Bachelet, who was charged with treason because he opposed the 1974 coup, was the father of Michelle Bachelet, who later became president of Chile. Ramon Caceres Jorquera and Edgar Ceballos Jones commanded the Air Force Academy, where Gen. Bachelet was tortured, The Santiago Times reported.
Justice Mario Carroza ruled Tuesday the two former colonels should be held for trial.
A report issued last month by the Legal Medical Service said Gen. Bachelet died of a heart attack caused by the treatment he was subjected to.
"Now it can be expected in our country that justice will be served," Angela Jeria, the general's widow, said. "It is healing and it helps a lot, because there are many people whose deaths have still not been investigated."
Michelle Bachelet and her mother were detained after the coup and then lived in exile for several years before returning to Chile. Bachelet served as president from 2006 to 2010.